You need to move the CA and CL names one character to the left
ATOM 6190 O HOH W 64 26.387 33.040 -0.685 1.00 40.92 O
ATOM 6191 CA CA B 1 37.417 44.961 41.022 1.00 12.13 CA
more like this..
Eleanor
Louise Gourlay wrote:
> ATOM 6189 O HOH W 63 14.409 51.932 0.124 1.00 46.53 O
> ATOM 6190 O HOH W 64 26.387 33.040 -0.685 1.00 40.92 O
> ATOM 6191 CA CA B 1 37.417 44.961 41.022 1.00 12.13 CA
> ATOM 6192 CA CA B 2 23.027 43.324 21.110 1.00 5.01 CA
> ATOM 6193 CA CA B 3 52.444 49.349 2.208 1.00 14.66 CA
> ATOM 6194 CA CA B 4 34.610 74.683 4.564 1.00 10.52 CA
> ATOM 6195 CL CL C 1 32.966 46.780 3.090 1.00 2.00 CL
> END
>
> I also tried Ca, Ca2+ but no luck. I added them to the structure with coot. Also, I forgot to say that the refinement works when I use another computer so it's something to do with mine.
> Thanks,
> Louise
>
> ----- Messaggio Originale -----
> Da: Louise Gourlay <[log in to unmask]>
> Data: Martedi', Agosto 19, 2008 4:26 pm
> Oggetto: [ccp4bb] Refmac problems on Mac OS X Leopard
> A: [log in to unmask]
>
>
>> Dear All,
>>
>> I installed CCP4 on my Mac OS X Leopard system using fink. I
>> have some problems with Refmac, it doesn't refine calcium or
>> chlorine atoms, or any non-protein atom in general. In the log
>> file it doesn't recognize them and says:
>> FORMATTED OLD file opened on unit 45
>> Logical name: ATOMSF, Filename: /sw/share/xtal/ccp4-
>> 6.0.2/lib/data/atomsf.lib No match for atom ID CL subtracting
>> one character
>> No match for atom ID CA subtracting one character
>>
>> Thanks,
>> Louise
>>
>>
>>
>>
>> ----- Messaggio Originale -----
>> Da: Garib Murshudov <[log in to unmask]>
>> Data: Mercoledi', Luglio 30, 2008 2:28 pm
>> Oggetto: Re: [ccp4bb] Preventing close contact between protein
>> and ligand
>> A: [log in to unmask]
>>
>>
>>> Dear Snageetha
>>>
>>> 1) Could you check please if specified atoms have zero
>>> occupancy.
>>> Atoms with zero occupancy are considered as absent and there
>>>
>> are
>>
>>> not
>>> restraints on them
>>> 2) symm y at the end of instructions means that the program
>>> check all
>>> possible symmetry operators and finds minimal distance. Most
>>> probably
>>> 5.024 is the distance between symmetry related atoms
>>> 3) to remove antibumping between different chains there is
>>> an
>>> undocumented keyword. It can be used. the keyword is (as an example)
>>>
>>> vdwrestraints exclude between chains A B
>>>
>>>
>>> Please let me know if this instruction does not work.
>>> NB: This option should not be used unless you know what you
>>>
>> are
>>
>>> doing
>>> (that is the reason why it has not been documented). If there
>>> are
>>> clashes between chains then there are reasons for that. For example
>>> if ligand has half occupancy then it is very likely that
>>> surrounding
>>> atoms also have multiple conformation and you should model them.
>>>
>>>
>>> regards
>>> Garib
>>>
>>>
>>> On 29 Jul 2008, at 18:24, Sangeetha Vedula wrote:
>>>
>>>
>>>> Dear bb users,
>>>>
>>>> I am refining a protein-ligand complex (at 1.68 A
>>>>
>> resolution)
>>
>>> in
>>>
>>>> which the ligand lies on a 2-fold crystallographic symmetry
>>>>
>>> axis.
>>>
>>>> The ligand occupancy is, therefore, 0.5 in each asymmetric unit.
>>>>
>>>> I am almost at the end of the refinement but one problem has
>>>>
>>> me
>>>
>>>> stumped. Refmac keeps moving a carbon in the ligand too
>>>>
>> close
>>
>>> to a
>>>
>>>> serine OG and an oxygen too close to an arginine CD. Given
>>>>
>>> that the
>>>
>>>> ligand is at the interface, the density is not perfect.
>>>>
>>> However, I
>>>
>>>> rebuild the ligand to eliminate close contacts and still be
>>>>
>>> within
>>>
>>>> density and refmac pulls it right back close to the protein.
>>>>
>>> The
>>>
>>>> refined position does not even look better than the rebuilt
>>>>
>>> one! It
>>>
>>>> almost always looks worse! Would refmac put less weight on
>>>>
>>> close
>>>
>>>> contacts with the ligand because it is only partially occupied?
>>>>
>>>> I tried to use external restraints between the ligand and
>>>>
>>> the
>>>
>>>> residues so that they are kept further away.
>>>>
>>>> Upon searching the net, I found this command line:
>>>>
>>>> external distance first chain [ch] residue [res] insertion
>>>>
>>> [ins] -
>>>
>>>> atom [n] [altcode [a]] second chain [ch] residue [res]
>>>>
>>> insertion
>>>
>>>> [ins]-
>>>> atom [n] [altcode [a] ] value [v] sigma [s] [symm y/n]
>>>>
>>>> I thought (hoped) that the distance herein is the minimum
>>>>
>>> distance
>>>
>>>> of approach between the specified atoms, I added these lines
>>>>
>>> from
>>>
>>>> within "Developer options" in refmac interface:
>>>>
>>>> exte dist first chain A resi 59 atom CD seco chain X resi
>>>>
>> 2001
>>
>>> atom
>>>
>>>> O1 valu 3.2 sigm 0.02 symm Y
>>>> exte dist first chain A resi 27 atom OG seco chain X resi
>>>>
>> 2001
>>
>>> atom
>>>
>>>> C10 valu 3.2 sigm 0.02 symm Y
>>>>
>>>> It didn't recognize these restraints at all.
>>>>
>>>> However, when I change these lines to:
>>>>
>>>> exte dist first chain A resi 59 atom CA seco chain X resi
>>>>
>> 2001
>>
>>> atom
>>>
>>>> O1 valu 3.2 sigm 0.02 symm Y
>>>> exte dist first chain A resi 27 atom OG seco chain X resi
>>>>
>> 2001
>>
>>> atom
>>>
>>>> C10 valu 3.2 sigm 0.02 symm Y
>>>>
>>>> Refmac recognizes the first line but not the second - lines
>>>>
>>> from
>>>
>>>> log file:
>>>>
>>>> Bond distance deviations from the ideal >10.000Sigma will be
>>>>
>>> monitored>
>>>
>>>> A 59 ARG CA . - X
>>>>
>>> 2001 DIE O1 . mod.= 5.024 id.= 3.200 dev=
>>>
>>>> -1.824 sig.= 0.020
>>>>
>>>> This raises two concerns:
>>>>
>>>> Concern 1: From the first line of output: the restraints
>>>>
>> here
>>
>>> don't
>>>
>>>> seem to be minimizing close contact at all; it seems to
>>>>
>> think
>>
>>> they
>>>
>>>> are bonded somehow (the distance between these atoms is not
>>>>
>>> 5.024;
>>>
>>>> it is 6.26 A; I don't know what 5.024 A is!).
>>>>
>>>> I am missing something here. It'd be great if someone can
>>>>
>> tell
>>
>>> me
>>>
>>>> what that is!
>>>>
>>>> Concern 2: This command only works when the first atom
>>>>
>>> specified is
>>>
>>>> a C-alpha atom (or maybe a main chain atom; I didn't try
>>>>
>>> using
>>>
>>>> other main chain atoms). Why is that?
>>>>
>>>> AND ULTIMATELY,
>>>>
>>>> is there some way I can tell refmac not to make the ligand
>>>>
>>> and
>>>
>>>> protein clash?
>>>>
>>>> I'd really appreciate any help!
>>>>
>>>> Thanks,
>>>>
>>>> Sangeetha.
>>>>
>>>
>> Louise Gourlay Ph.D Dep. of Biomolecular Sciences and
>> Biotechnology, Università degli Studi di Milano Via Celoria 26
>> Milano 20133 http://users.unimi.it/biolstru/Home.html Italy
>>
>>
>>
>>
>
> Louise Gourlay Ph.D Dep. of Biomolecular Sciences and Biotechnology, Università degli Studi di Milano Via Celoria 26 Milano 20133 http://users.unimi.it/biolstru/Home.html Italy
>
>
>
>
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